# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. # # This program is free software: you can redistribute it and/or modify it # under the terms of the GNU Affero General Public License # as published by the Free Software Foundation, either version 3 of the # License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. # See the GNU Affero General Public License for more details. # # This program is available from Source Forge: at GeneNetwork Project # (sourceforge.net/projects/genenetwork/). # # Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) # at rwilliams@uthsc.edu and xzhou15@uthsc.edu # # This module is used by GeneNetwork project (www.genenetwork.org) from dataclasses import dataclass from dataclasses import field from dataclasses import InitVar from typing import Optional, Dict, List from db.call import fetchall, fetchone, fetch1 from utility.logger import getLogger from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL from db.gn_server import menu_main from pprint import pformat as pf from utility.db_tools import escape from utility.db_tools import mescape from utility.db_tools import create_in_clause from maintenance import get_group_samplelists from utility.tools import locate, locate_ignore_error, flat_files from utility import gen_geno_ob from utility import chunks from utility.benchmark import Bench from utility import webqtlUtil from db import webqtlDatabaseFunction from base import species from base import webqtlConfig from flask import Flask, g from base.webqtlConfig import TMPDIR from urllib.parse import urlparse from utility.tools import SQL_URI import os import math import string import collections import codecs import json import requests import gzip import pickle as pickle import itertools import hashlib import datetime from redis import Redis r = Redis() logger = getLogger(__name__) # Used by create_database to instantiate objects # Each subclass will add to this DS_NAME_MAP = {} def create_dataset(dataset_name, dataset_type=None, get_samplelist=True, group_name=None): if dataset_name == "Temp": dataset_type = "Temp" if not dataset_type: dataset_type = Dataset_Getter(dataset_name) dataset_ob = DS_NAME_MAP[dataset_type] dataset_class = globals()[dataset_ob] if dataset_type == "Temp": return dataset_class(dataset_name, get_samplelist, group_name) else: return dataset_class(dataset_name, get_samplelist) @dataclass class DatasetType: """Create a dictionary of samples where the value is set to Geno, Publish or ProbeSet. E.g. {'AD-cases-controls-MyersGeno': 'Geno', 'AD-cases-controls-MyersPublish': 'Publish', 'AKXDGeno': 'Geno', 'AXBXAGeno': 'Geno', 'AXBXAPublish': 'Publish', 'Aging-Brain-UCIPublish': 'Publish', 'All Phenotypes': 'Publish', 'B139_K_1206_M': 'ProbeSet', 'B139_K_1206_R': 'ProbeSet' ... } """ redis_instance: InitVar[Redis] datasets: Optional[Dict] = field(init=False, default_factory=dict) data: Optional[Dict] = field(init=False) def __post_init__(self, redis_instance): self.redis_instance = redis_instance data = redis_instance.get("dataset_structure") if data: self.datasets = json.loads(data) else: # ZS: I don't think this should ever run unless Redis is # emptied try: data = json.loads(requests.get( GN2_BASE_URL + "/api/v_pre1/gen_dropdown", timeout=5).content) for _species in data['datasets']: for group in data['datasets'][_species]: for dataset_type in data['datasets'][_species][group]: for dataset in data['datasets'][_species][group][dataset_type]: short_dataset_name = dataset[1] if dataset_type == "Phenotypes": new_type = "Publish" elif dataset_type == "Genotypes": new_type = "Geno" else: new_type = "ProbeSet" self.datasets[short_dataset_name] = new_type except Exception: # Do nothing pass self.redis_instance.set("dataset_structure", json.dumps(self.datasets)) self.data = data def set_dataset_key(self, t, name): """If name is not in the object's dataset dictionary, set it, and update dataset_structure in Redis args: t: Type of dataset structure which can be: 'mrna_expr', 'pheno', 'other_pheno', 'geno' name: The name of the key to inserted in the datasets dictionary """ sql_query_mapping = { 'mrna_expr': ("SELECT ProbeSetFreeze.Id FROM " "ProbeSetFreeze WHERE " "ProbeSetFreeze.Name = \"%s\" "), 'pheno': ("SELECT InfoFiles.GN_AccesionId " "FROM InfoFiles, PublishFreeze, InbredSet " "WHERE InbredSet.Name = '%s' AND " "PublishFreeze.InbredSetId = InbredSet.Id AND " "InfoFiles.InfoPageName = PublishFreeze.Name"), 'other_pheno': ("SELECT PublishFreeze.Name " "FROM PublishFreeze, InbredSet " "WHERE InbredSet.Name = '%s' AND " "PublishFreeze.InbredSetId = InbredSet.Id"), 'geno': ("SELECT GenoFreeze.Id FROM GenoFreeze WHERE " "GenoFreeze.Name = \"%s\" ") } dataset_name_mapping = { "mrna_expr": "ProbeSet", "pheno": "Publish", "other_pheno": "Publish", "geno": "Geno", } group_name = name if t in ['pheno', 'other_pheno']: group_name = name.replace("Publish", "") results = g.db.execute(sql_query_mapping[t] % group_name).fetchone() if results: self.datasets[name] = dataset_name_mapping[t] self.redis_instance.set( "dataset_structure", json.dumps(self.datasets)) return True return None def __call__(self, name): if name not in self.datasets: for t in ["mrna_expr", "pheno", "other_pheno", "geno"]: # This has side-effects, with the end result being a # truth-y value if(self.set_dataset_key(t, name)): break # Return None if name has not been set return self.datasets.get(name, None) # Do the intensive work at startup one time only Dataset_Getter = DatasetType(r) def create_datasets_list(): if USE_REDIS: key = "all_datasets" result = r.get(key) if result: logger.debug("Redis cache hit") datasets = pickle.loads(result) if result is None: datasets = list() with Bench("Creating DataSets object"): type_dict = {'Publish': 'PublishFreeze', 'ProbeSet': 'ProbeSetFreeze', 'Geno': 'GenoFreeze'} for dataset_type in type_dict: query = "SELECT Name FROM {}".format(type_dict[dataset_type]) for result in fetchall(query): # The query at the beginning of this function isn't # necessary here, but still would rather just reuse # it logger.debug("type: {}\tname: # {}".format(dataset_type, result.Name)) dataset = create_dataset(result.Name, dataset_type) datasets.append(dataset) if USE_REDIS: r.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL)) r.expire(key, 60 * 60) return datasets class Markers: """Todo: Build in cacheing so it saves us reading the same file more than once""" def __init__(self, name): json_data_fh = open(locate(name + ".json", 'genotype/json')) markers = [] with open("%s/%s_snps.txt" % (flat_files('genotype/bimbam'), name), 'r') as bimbam_fh: if len(bimbam_fh.readline().split(", ")) > 2: delimiter = ", " elif len(bimbam_fh.readline().split(",")) > 2: delimiter = "," elif len(bimbam_fh.readline().split("\t")) > 2: delimiter = "\t" else: delimiter = " " for line in bimbam_fh: marker = {} marker['name'] = line.split(delimiter)[0].rstrip() marker['Mb'] = float(line.split(delimiter)[ 1].rstrip()) / 1000000 marker['chr'] = line.split(delimiter)[2].rstrip() markers.append(marker) for marker in markers: if (marker['chr'] != "X") and (marker['chr'] != "Y") and (marker['chr'] != "M"): marker['chr'] = int(marker['chr']) marker['Mb'] = float(marker['Mb']) self.markers = markers def add_pvalues(self, p_values): logger.debug("length of self.markers:", len(self.markers)) logger.debug("length of p_values:", len(p_values)) if isinstance(p_values, list): # THIS IS only needed for the case when we are limiting the number of p-values calculated # if len(self.markers) > len(p_values): # self.markers = self.markers[:len(p_values)] for marker, p_value in zip(self.markers, p_values): if not p_value: continue marker['p_value'] = float(p_value) if math.isnan(marker['p_value']) or marker['p_value'] <= 0: marker['lod_score'] = 0 marker['lrs_value'] = 0 else: marker['lod_score'] = -math.log10(marker['p_value']) # Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61 elif isinstance(p_values, dict): filtered_markers = [] for marker in self.markers: if marker['name'] in p_values: marker['p_value'] = p_values[marker['name']] if math.isnan(marker['p_value']) or (marker['p_value'] <= 0): marker['lod_score'] = 0 marker['lrs_value'] = 0 else: marker['lod_score'] = -math.log10(marker['p_value']) # Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values marker['lrs_value'] = - \ math.log10(marker['p_value']) * 4.61 filtered_markers.append(marker) self.markers = filtered_markers class HumanMarkers(Markers): def __init__(self, name, specified_markers=[]): marker_data_fh = open(flat_files('mapping') + '/' + name + '.bim') self.markers = [] for line in marker_data_fh: splat = line.strip().split() if len(specified_markers) > 0: if splat[1] in specified_markers: marker = {} marker['chr'] = int(splat[0]) marker['name'] = splat[1] marker['Mb'] = float(splat[3]) / 1000000 else: continue else: marker = {} marker['chr'] = int(splat[0]) marker['name'] = splat[1] marker['Mb'] = float(splat[3]) / 1000000 self.markers.append(marker) def add_pvalues(self, p_values): super(HumanMarkers, self).add_pvalues(p_values) class DatasetGroup: """ Each group has multiple datasets; each species has multiple groups. For example, Mouse has multiple groups (BXD, BXA, etc), and each group has multiple datasets associated with it. """ def __init__(self, dataset, name=None): """This sets self.group and self.group_id""" if name == None: self.name, self.id, self.genetic_type, self.code = fetchone( dataset.query_for_group) else: self.name, self.id, self.genetic_type, self.code = fetchone( "SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode FROM InbredSet where Name='%s'" % name) if self.name == 'BXD300': self.name = "BXD" self.f1list = None self.parlist = None self.get_f1_parent_strains() self.mapping_id, self.mapping_names = self.get_mapping_methods() self.species = webqtlDatabaseFunction.retrieve_species(self.name) self.incparentsf1 = False self.allsamples = None self._datasets = None self.genofile = None def get_mapping_methods(self): mapping_id = g.db.execute( "select MappingMethodId from InbredSet where Name= '%s'" % self.name).fetchone()[0] if mapping_id == "1": mapping_names = ["GEMMA", "QTLReaper", "R/qtl"] elif mapping_id == "2": mapping_names = ["GEMMA"] elif mapping_id == "3": mapping_names = ["R/qtl"] elif mapping_id == "4": mapping_names = ["GEMMA", "PLINK"] else: mapping_names = [] return mapping_id, mapping_names def get_markers(self): def check_plink_gemma(): if flat_file_exists("mapping"): MAPPING_PATH = flat_files("mapping") + "/" if os.path.isfile(MAPPING_PATH + self.name + ".bed"): return True return False if check_plink_gemma(): marker_class = HumanMarkers else: marker_class = Markers if self.genofile: self.markers = marker_class(self.genofile[:-5]) else: self.markers = marker_class(self.name) def get_f1_parent_strains(self): try: # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; f1, f12, maternal, paternal = webqtlUtil.ParInfo[self.name] except KeyError: f1 = f12 = maternal = paternal = None if f1 and f12: self.f1list = [f1, f12] if maternal and paternal: self.parlist = [maternal, paternal] def get_study_samplelists(self): study_sample_file = locate_ignore_error( self.name + ".json", 'study_sample_lists') try: f = open(study_sample_file) except: return [] study_samples = json.load(f) return study_samples def get_genofiles(self): jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, self.name) try: f = open(jsonfile) except: return None jsondata = json.load(f) return jsondata['genofile'] def get_samplelist(self): result = None key = "samplelist:v3:" + self.name if USE_REDIS: result = r.get(key) if result is not None: self.samplelist = json.loads(result) else: genotype_fn = locate_ignore_error(self.name + ".geno", 'genotype') if genotype_fn: self.samplelist = get_group_samplelists.get_samplelist( "geno", genotype_fn) else: self.samplelist = None if USE_REDIS: r.set(key, json.dumps(self.samplelist)) r.expire(key, 60 * 5) def all_samples_ordered(self): result = [] lists = (self.parlist, self.f1list, self.samplelist) [result.extend(l) for l in lists if l] return result def read_genotype_file(self, use_reaper=False): '''Read genotype from .geno file instead of database''' # genotype_1 is Dataset Object without parents and f1 # genotype_2 is Dataset Object with parents and f1 (not for intercross) # reaper barfs on unicode filenames, so here we ensure it's a string if self.genofile: if "RData" in self.genofile: # ZS: This is a temporary fix; I need to change the way the JSON files that point to multiple genotype files are structured to point to other file types like RData full_filename = str( locate(self.genofile.split(".")[0] + ".geno", 'genotype')) else: full_filename = str(locate(self.genofile, 'genotype')) else: full_filename = str(locate(self.name + '.geno', 'genotype')) genotype_1 = gen_geno_ob.genotype(full_filename) if genotype_1.type == "group" and self.parlist: genotype_2 = genotype_1.add( Mat=self.parlist[0], Pat=self.parlist[1]) # , F1=_f1) else: genotype_2 = genotype_1 # determine default genotype object if self.incparentsf1 and genotype_1.type != "intercross": genotype = genotype_2 else: self.incparentsf1 = 0 genotype = genotype_1 self.samplelist = list(genotype.prgy) return genotype def datasets(group_name, this_group=None): key = "group_dataset_menu:v2:" + group_name dataset_menu = [] the_results = fetchall(''' (SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name FROM PublishFreeze,InbredSet WHERE PublishFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = '%s' ORDER BY PublishFreeze.Id ASC) UNION (SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name FROM GenoFreeze, InbredSet WHERE GenoFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = '%s') UNION (SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name like %s ORDER BY Tissue.Name, ProbeSetFreeze.OrderList DESC) ''' % (group_name, group_name, "'" + group_name + "'")) sorted_results = sorted(the_results, key=lambda kv: kv[0]) # ZS: This is kind of awkward, but need to ensure Phenotypes show up before Genotypes in dropdown pheno_inserted = False geno_inserted = False for dataset_item in sorted_results: tissue_name = dataset_item[0] dataset = dataset_item[1] dataset_short = dataset_item[2] if tissue_name in ['#PublishFreeze', '#GenoFreeze']: if tissue_name == '#PublishFreeze' and (dataset_short == group_name + 'Publish'): dataset_menu.insert( 0, dict(tissue=None, datasets=[(dataset, dataset_short)])) pheno_inserted = True elif pheno_inserted and tissue_name == '#GenoFreeze': dataset_menu.insert( 1, dict(tissue=None, datasets=[(dataset, dataset_short)])) geno_inserted = True else: dataset_menu.append( dict(tissue=None, datasets=[(dataset, dataset_short)])) else: tissue_already_exists = False for i, tissue_dict in enumerate(dataset_menu): if tissue_dict['tissue'] == tissue_name: tissue_already_exists = True break if tissue_already_exists: dataset_menu[i]['datasets'].append((dataset, dataset_short)) else: dataset_menu.append(dict(tissue=tissue_name, datasets=[(dataset, dataset_short)])) if USE_REDIS: r.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL)) r.expire(key, 60 * 5) if this_group != None: this_group._datasets = dataset_menu return this_group._datasets else: return dataset_menu class DataSet: """ DataSet class defines a dataset in webqtl, can be either Microarray, Published phenotype, genotype, or user input dataset(temp) """ def __init__(self, name, get_samplelist=True, group_name=None): assert name, "Need a name" self.name = name self.id = None self.shortname = None self.fullname = None self.type = None self.data_scale = None # ZS: For example log2 self.accession_id = None self.setup() if self.type == "Temp": # Need to supply group name as input if temp trait # sets self.group and self.group_id and gets genotype self.group = DatasetGroup(self, name=group_name) else: self.check_confidentiality() self.retrieve_other_names() # sets self.group and self.group_id and gets genotype self.group = DatasetGroup(self) self.accession_id = self.get_accession_id() if get_samplelist == True: self.group.get_samplelist() self.species = species.TheSpecies(self) def as_dict(self): return { 'name': self.name, 'shortname': self.shortname, 'fullname': self.fullname, 'type': self.type, 'data_scale': self.data_scale, 'group': self.group.name, 'accession_id': self.accession_id } def get_accession_id(self): if self.type == "Publish": results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where InbredSet.Name = %s and PublishFreeze.InbredSetId = InbredSet.Id and InfoFiles.InfoPageName = PublishFreeze.Name and PublishFreeze.public > 0 and PublishFreeze.confidentiality < 1 order by PublishFreeze.CreateTime desc""", (self.group.name)).fetchone() elif self.type == "Geno": results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, GenoFreeze, InbredSet where InbredSet.Name = %s and GenoFreeze.InbredSetId = InbredSet.Id and InfoFiles.InfoPageName = GenoFreeze.ShortName and GenoFreeze.public > 0 and GenoFreeze.confidentiality < 1 order by GenoFreeze.CreateTime desc""", (self.group.name)).fetchone() else: results = None if results != None: return str(results[0]) else: return "None" def retrieve_other_names(self): """This method fetches the the dataset names in search_result. If the data set name parameter is not found in the 'Name' field of the data set table, check if it is actually the FullName or ShortName instead. This is not meant to retrieve the data set info if no name at all is passed. """ try: if self.type == "ProbeSet": query_args = tuple(escape(x) for x in ( self.name, self.name, self.name)) self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = fetch1(""" SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name FROM ProbeSetFreeze, ProbeFreeze, Tissue WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND ProbeFreeze.TissueId = Tissue.Id AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s') """ % (query_args), "/dataset/" + self.name + ".json", lambda r: (r["id"], r["name"], r["full_name"], r["short_name"], r["data_scale"], r["tissue"]) ) else: query_args = tuple(escape(x) for x in ( (self.type + "Freeze"), self.name, self.name, self.name)) self.tissue = "N/A" self.id, self.name, self.fullname, self.shortname = fetchone(""" SELECT Id, Name, FullName, ShortName FROM %s WHERE (Name = '%s' OR FullName = '%s' OR ShortName = '%s') """ % (query_args)) except TypeError: logger.debug( "Dataset {} is not yet available in GeneNetwork.".format(self.name)) pass def chunk_dataset(self, dataset, n): results = {} query = """ SELECT ProbeSetXRef.DataId,ProbeSet.Name FROM ProbeSet, ProbeSetXRef, ProbeSetFreeze WHERE ProbeSetFreeze.Name = '{}' AND ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND ProbeSetXRef.ProbeSetId = ProbeSet.Id """.format(self.name) # should cache this traits_name_dict = dict(g.db.execute(query).fetchall()) for i in range(0, len(dataset), n): matrix = list(dataset[i:i + n]) trait_name = traits_name_dict[matrix[0][0]] my_values = [value for (trait_name, strain, value) in matrix] results[trait_name] = my_values return results def get_probeset_data(self, sample_list=None, trait_ids=None): # improvement of get trait data--->>> if sample_list: self.samplelist = sample_list else: self.samplelist = self.group.samplelist if self.group.parlist != None and self.group.f1list != None: if (self.group.parlist + self.group.f1list) in self.samplelist: self.samplelist += self.group.parlist + self.group.f1list query = """ SELECT Strain.Name, Strain.Id FROM Strain, Species WHERE Strain.Name IN {} and Strain.SpeciesId=Species.Id and Species.name = '{}' """.format(create_in_clause(self.samplelist), *mescape(self.group.species)) results = dict(g.db.execute(query).fetchall()) sample_ids = [results[item] for item in self.samplelist] sorted_samplelist = [strain_name for strain_name, strain_id in sorted( results.items(), key=lambda item: item[1])] query = """SELECT * from ProbeSetData where StrainID in {} and id in (SELECT ProbeSetXRef.DataId FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze) WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and ProbeSetFreeze.Name = '{}' and ProbeSet.Id = ProbeSetXRef.ProbeSetId)""".format(create_in_clause(sample_ids), self.name) query_results = list(g.db.execute(query).fetchall()) data_results = self.chunk_dataset(query_results, len(sample_ids)) self.samplelist = sorted_samplelist self.trait_data = data_results def get_trait_data(self, sample_list=None): if sample_list: self.samplelist = sample_list else: self.samplelist = self.group.samplelist if self.group.parlist != None and self.group.f1list != None: if (self.group.parlist + self.group.f1list) in self.samplelist: self.samplelist += self.group.parlist + self.group.f1list query = """ SELECT Strain.Name, Strain.Id FROM Strain, Species WHERE Strain.Name IN {} and Strain.SpeciesId=Species.Id and Species.name = '{}' """.format(create_in_clause(self.samplelist), *mescape(self.group.species)) results = dict(g.db.execute(query).fetchall()) sample_ids = [results.get(item) for item in self.samplelist if item is not None] # MySQL limits the number of tables that can be used in a join to 61, # so we break the sample ids into smaller chunks # Postgres doesn't have that limit, so we can get rid of this after we transition chunk_size = 50 number_chunks = int(math.ceil(len(sample_ids) / chunk_size)) cached_results = fetch_cached_results(self.name, self.type, self.samplelist) if cached_results is None: trait_sample_data = [] for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks): if self.type == "Publish": dataset_type = "Phenotype" else: dataset_type = self.type temp = ['T%s.value' % item for item in sample_ids_step] if self.type == "Publish": query = "SELECT {}XRef.Id,".format(escape(self.type)) else: query = "SELECT {}.Name,".format(escape(dataset_type)) data_start_pos = 1 query += ', '.join(temp) query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(dataset_type, self.type, self.type)) for item in sample_ids_step: query += """ left join {}Data as T{} on T{}.Id = {}XRef.DataId and T{}.StrainId={}\n """.format(*mescape(self.type, item, item, self.type, item, item)) if self.type == "Publish": query += """ WHERE {}XRef.InbredSetId = {}Freeze.InbredSetId and {}Freeze.Name = '{}' and {}.Id = {}XRef.{}Id order by {}.Id """.format(*mescape(self.type, self.type, self.type, self.name, dataset_type, self.type, dataset_type, dataset_type)) else: query += """ WHERE {}XRef.{}FreezeId = {}Freeze.Id and {}Freeze.Name = '{}' and {}.Id = {}XRef.{}Id order by {}.Id """.format(*mescape(self.type, self.type, self.type, self.type, self.name, dataset_type, self.type, self.type, dataset_type)) results = g.db.execute(query).fetchall() trait_sample_data.append([list(result) for result in results]) trait_count = len(trait_sample_data[0]) self.trait_data = collections.defaultdict(list) data_start_pos = 1 for trait_counter in range(trait_count): trait_name = trait_sample_data[0][trait_counter][0] for chunk_counter in range(int(number_chunks)): self.trait_data[trait_name] += ( trait_sample_data[chunk_counter][trait_counter][data_start_pos:]) cache_dataset_results( self.name, self.type, self.samplelist, self.trait_data) else: self.trait_data = cached_results class PhenotypeDataSet(DataSet): DS_NAME_MAP['Publish'] = 'PhenotypeDataSet' def setup(self): # Fields in the database table self.search_fields = ['Phenotype.Post_publication_description', 'Phenotype.Pre_publication_description', 'Phenotype.Pre_publication_abbreviation', 'Phenotype.Post_publication_abbreviation', 'PublishXRef.mean', 'Phenotype.Lab_code', 'Publication.PubMed_ID', 'Publication.Abstract', 'Publication.Title', 'Publication.Authors', 'PublishXRef.Id'] # Figure out what display_fields is self.display_fields = ['name', 'group_code', 'pubmed_id', 'pre_publication_description', 'post_publication_description', 'original_description', 'pre_publication_abbreviation', 'post_publication_abbreviation', 'mean', 'lab_code', 'submitter', 'owner', 'authorized_users', 'authors', 'title', 'abstract', 'journal', 'volume', 'pages', 'month', 'year', 'sequence', 'units', 'comments'] # Fields displayed in the search results table header self.header_fields = ['Index', 'Record', 'Description', 'Authors', 'Year', 'Max LRS', 'Max LRS Location', 'Additive Effect'] self.type = 'Publish' self.query_for_group = ''' SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode FROM InbredSet, PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id AND PublishFreeze.Name = "%s" ''' % escape(self.name) def check_confidentiality(self): # (Urgently?) Need to write this pass def get_trait_info(self, trait_list, species=''): for this_trait in trait_list: if not this_trait.haveinfo: this_trait.retrieve_info(get_qtl_info=True) description = this_trait.post_publication_description # If the dataset is confidential and the user has access to confidential # phenotype traits, then display the pre-publication description instead # of the post-publication description if this_trait.confidential: this_trait.description_display = "" continue # for now, because no authorization features if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait( privilege=self.privilege, userName=self.userName, authorized_users=this_trait.authorized_users): description = this_trait.pre_publication_description if len(description) > 0: this_trait.description_display = description.strip() else: this_trait.description_display = "" if not this_trait.year.isdigit(): this_trait.pubmed_text = "N/A" else: this_trait.pubmed_text = this_trait.year if this_trait.pubmed_id: this_trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id # LRS and its location this_trait.LRS_score_repr = "N/A" this_trait.LRS_location_repr = "N/A" if this_trait.lrs: query = """ select Geno.Chr, Geno.Mb from Geno, Species where Species.Name = '%s' and Geno.Name = '%s' and Geno.SpeciesId = Species.Id """ % (species, this_trait.locus) result = g.db.execute(query).fetchone() if result: if result[0] and result[1]: LRS_Chr = result[0] LRS_Mb = result[1] this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % ( LRS_Chr, float(LRS_Mb)) def retrieve_sample_data(self, trait): query = """ SELECT Strain.Name, PublishData.value, PublishSE.error, NStrain.count, Strain.Name2 FROM (PublishData, Strain, PublishXRef, PublishFreeze) left join PublishSE on (PublishSE.DataId = PublishData.Id AND PublishSE.StrainId = PublishData.StrainId) left join NStrain on (NStrain.DataId = PublishData.Id AND NStrain.StrainId = PublishData.StrainId) WHERE PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND PublishFreeze.Id = %s AND PublishData.StrainId = Strain.Id Order BY Strain.Name """ results = g.db.execute(query, (trait, self.id)).fetchall() return results class GenotypeDataSet(DataSet): DS_NAME_MAP['Geno'] = 'GenotypeDataSet' def setup(self): # Fields in the database table self.search_fields = ['Name', 'Chr'] # Find out what display_fields is self.display_fields = ['name', 'chr', 'mb', 'source2', 'sequence'] # Fields displayed in the search results table header self.header_fields = ['Index', 'ID', 'Location'] # Todo: Obsolete or rename this field self.type = 'Geno' self.query_for_group = ''' SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode FROM InbredSet, GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id AND GenoFreeze.Name = "%s" ''' % escape(self.name) def check_confidentiality(self): return geno_mrna_confidentiality(self) def get_trait_info(self, trait_list, species=None): for this_trait in trait_list: if not this_trait.haveinfo: this_trait.retrieveInfo() if this_trait.chr and this_trait.mb: this_trait.location_repr = 'Chr%s: %.6f' % ( this_trait.chr, float(this_trait.mb)) def retrieve_sample_data(self, trait): query = """ SELECT Strain.Name, GenoData.value, GenoSE.error, "N/A", Strain.Name2 FROM (GenoData, GenoFreeze, Strain, Geno, GenoXRef) left join GenoSE on (GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId) WHERE Geno.SpeciesId = %s AND Geno.Name = %s AND GenoXRef.GenoId = Geno.Id AND GenoXRef.GenoFreezeId = GenoFreeze.Id AND GenoFreeze.Name = %s AND GenoXRef.DataId = GenoData.Id AND GenoData.StrainId = Strain.Id Order BY Strain.Name """ results = g.db.execute(query, (webqtlDatabaseFunction.retrieve_species_id(self.group.name), trait, self.name)).fetchall() if self.group.name in webqtlUtil.ParInfo: f1_1, f1_2, ref, nonref = webqtlUtil.ParInfo[self.group.name] results.append([f1_1, 0, None, "N/A", f1_1]) results.append([f1_2, 0, None, "N/A", f1_2]) results.append([ref, -1, None, "N/A", ref]) results.append([nonref, 1, None, "N/A", nonref]) return results class MrnaAssayDataSet(DataSet): ''' An mRNA Assay is a quantitative assessment (assay) associated with an mRNA trait This used to be called ProbeSet, but that term only refers specifically to the Affymetrix platform and is far too specific. ''' DS_NAME_MAP['ProbeSet'] = 'MrnaAssayDataSet' def setup(self): # Fields in the database table self.search_fields = ['Name', 'Description', 'Probe_Target_Description', 'Symbol', 'Alias', 'GenbankId', 'UniGeneId', 'RefSeq_TranscriptId'] # Find out what display_fields is self.display_fields = ['name', 'symbol', 'description', 'probe_target_description', 'chr', 'mb', 'alias', 'geneid', 'genbankid', 'unigeneid', 'omim', 'refseq_transcriptid', 'blatseq', 'targetseq', 'chipid', 'comments', 'strand_probe', 'strand_gene', 'proteinid', 'uniprotid', 'probe_set_target_region', 'probe_set_specificity', 'probe_set_blat_score', 'probe_set_blat_mb_start', 'probe_set_blat_mb_end', 'probe_set_strand', 'probe_set_note_by_rw', 'flag'] # Fields displayed in the search results table header self.header_fields = ['Index', 'Record', 'Symbol', 'Description', 'Location', 'Mean', 'Max LRS', 'Max LRS Location', 'Additive Effect'] # Todo: Obsolete or rename this field self.type = 'ProbeSet' self.query_for_group = ''' SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode FROM InbredSet, ProbeSetFreeze, ProbeFreeze WHERE ProbeFreeze.InbredSetId = InbredSet.Id AND ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND ProbeSetFreeze.Name = "%s" ''' % escape(self.name) def check_confidentiality(self): return geno_mrna_confidentiality(self) def get_trait_info(self, trait_list=None, species=''): # Note: setting trait_list to [] is probably not a great idea. if not trait_list: trait_list = [] for this_trait in trait_list: if not this_trait.haveinfo: this_trait.retrieveInfo(QTL=1) if not this_trait.symbol: this_trait.symbol = "N/A" # XZ, 12/08/2008: description # XZ, 06/05/2009: Rob asked to add probe target description description_string = str( str(this_trait.description).strip(codecs.BOM_UTF8), 'utf-8') target_string = str( str(this_trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') if len(description_string) > 1 and description_string != 'None': description_display = description_string else: description_display = this_trait.symbol if (len(description_display) > 1 and description_display != 'N/A' and len(target_string) > 1 and target_string != 'None'): description_display = description_display + '; ' + target_string.strip() # Save it for the jinja2 template this_trait.description_display = description_display if this_trait.chr and this_trait.mb: this_trait.location_repr = 'Chr%s: %.6f' % ( this_trait.chr, float(this_trait.mb)) # Get mean expression value query = ( """select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet where ProbeSetXRef.ProbeSetFreezeId = %s and ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSet.Name = '%s' """ % (escape(str(this_trait.dataset.id)), escape(this_trait.name))) result = g.db.execute(query).fetchone() mean = result[0] if result else 0 if mean: this_trait.mean = "%2.3f" % mean # LRS and its location this_trait.LRS_score_repr = 'N/A' this_trait.LRS_location_repr = 'N/A' # Max LRS and its Locus location if this_trait.lrs and this_trait.locus: query = """ select Geno.Chr, Geno.Mb from Geno, Species where Species.Name = '{}' and Geno.Name = '{}' and Geno.SpeciesId = Species.Id """.format(species, this_trait.locus) result = g.db.execute(query).fetchone() if result: lrs_chr, lrs_mb = result this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs this_trait.LRS_location_repr = 'Chr%s: %.6f' % ( lrs_chr, float(lrs_mb)) return trait_list def retrieve_sample_data(self, trait): query = """ SELECT Strain.Name, ProbeSetData.value, ProbeSetSE.error, NStrain.count, Strain.Name2 FROM (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef) left join ProbeSetSE on (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId) left join NStrain on (NStrain.DataId = ProbeSetData.Id AND NStrain.StrainId = ProbeSetData.StrainId) WHERE ProbeSet.Name = '%s' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND ProbeSetFreeze.Name = '%s' AND ProbeSetXRef.DataId = ProbeSetData.Id AND ProbeSetData.StrainId = Strain.Id Order BY Strain.Name """ % (escape(trait), escape(self.name)) results = g.db.execute(query).fetchall() return results def retrieve_genes(self, column_name): query = """ select ProbeSet.Name, ProbeSet.%s from ProbeSet,ProbeSetXRef where ProbeSetXRef.ProbeSetFreezeId = %s and ProbeSetXRef.ProbeSetId=ProbeSet.Id; """ % (column_name, escape(str(self.id))) results = g.db.execute(query).fetchall() return dict(results) class TempDataSet(DataSet): '''Temporary user-generated data set''' DS_NAME_MAP['Temp'] = 'TempDataSet' def setup(self): self.search_fields = ['name', 'description'] self.display_fields = ['name', 'description'] self.header_fields = ['Name', 'Description'] self.type = 'Temp' # Need to double check later how these are used self.id = 1 self.fullname = 'Temporary Storage' self.shortname = 'Temp' def geno_mrna_confidentiality(ob): dataset_table = ob.type + "Freeze" query = '''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name) result = g.db.execute(query) (dataset_id, name, full_name, confidential, authorized_users) = result.fetchall()[0] if confidential: return True result = g.db.execute(query) (dataset_id, name, full_name, confidential, authorized_users) = result.fetchall()[0] if confidential: return True def parse_db_url(): parsed_db = urlparse(SQL_URI) return (parsed_db.hostname, parsed_db.username, parsed_db.password, parsed_db.path[1:]) def query_table_timestamp(dataset_type: str): """function to query the update timestamp of a given dataset_type""" # computation data and actions fetch_db_name = parse_db_url() query_update_time = f""" SELECT UPDATE_TIME FROM information_schema.tables WHERE TABLE_SCHEMA = '{fetch_db_name[-1]}' AND TABLE_NAME = '{dataset_type}Data' """ date_time_obj = g.db.execute(query_update_time).fetchone()[0] return date_time_obj.strftime("%Y-%m-%d %H:%M:%S") def generate_hash_file(dataset_name: str, dataset_type: str, dataset_timestamp: str, samplelist: str): """given the trait_name generate a unique name for this""" string_unicode = f"{dataset_name}{dataset_timestamp}{samplelist}".encode() md5hash = hashlib.md5(string_unicode) return md5hash.hexdigest() def cache_dataset_results(dataset_name: str, dataset_type: str, samplelist: List, query_results: List): """function to cache dataset query results to file input dataset_name and type query_results(already processed in default dict format) """ # data computations actions # store the file path on redis table_timestamp = query_table_timestamp(dataset_type) samplelist_as_str = ",".join(samplelist) file_name = generate_hash_file(dataset_name, dataset_type, table_timestamp, samplelist_as_str) file_path = os.path.join(TMPDIR, f"{file_name}.json") with open(file_path, "w") as file_handler: json.dump(query_results, file_handler) def fetch_cached_results(dataset_name: str, dataset_type: str, samplelist: List): """function to fetch the cached results""" table_timestamp = query_table_timestamp(dataset_type) samplelist_as_str = ",".join(samplelist) file_name = generate_hash_file(dataset_name, dataset_type, table_timestamp, samplelist_as_str) file_path = os.path.join(TMPDIR, f"{file_name}.json") try: with open(file_path, "r") as file_handler: return json.load(file_handler) except Exception: pass